write documentation

Author: jslit

.gradle/7.5.1/executionHistory/executionHistory.bin

@@ -1,5 +1,56 @@
 # bamscope
-<img
-  src="example.png"
-  alt="Alt text"
-  style="display: inline-block; margin: 0 auto; max-width: 300px">
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://github.com/jslfree080/bamscope/blob/main/LICENSE)
+
+<img alt="demonstration" src="https://github.com/jslfree080/jslfree080/blob/main/example2.png" width=550>
+
+A command line tool (in Kotlin/JVM) for visualizing BAM alignments.
+
+## Prerequisites
+
+Bamscope requires **Java 11** or later versions to build and run.
+
+Also, [samtools](https://github.com/samtools/samtools) should be pre-installed to support accessing file formats such as BAM and FASTA.
+
+## Building
+
+* Clone the repo:
+```
+    git clone https://github.com/jslfree080/bamscope.git
+    cd bamscope/
+```
+
+* Build an executable Bamscope jar with all dependencies packaged:
+```
+    ./gradlew build
+```
+
+## Usage
+
+### Command line
+
+The resulting jar will be in `build/libs`.
+
+```
+Usage: java -jar build/libs/bamscope.jar <chrPos> <bamPath> [options]
+
+Parameters:
+      <chrPos>              Input chromosomal position.      ex) (chr)N:XXXXXXXX
+      <bamPath>             Path to an indexed bam file.       ex) path/to/x.bam
+     
+Options:
+  -f, --format=<format>     File format of an output image.         default) png
+  -h, --help                Show this help message and exit.
+  -o, --outPath=<outPath>   Path to an output image.                  default) .
+  -r, --refPath=<refPath>   Path to a reference fasta.       ex) path/to/x.fasta
+  -s, --sPath=<sPath>       Path to the samtools.    ex) /usr/local/bin/samtools
+  -w, --width=<width>       Width of start to interest position.     default) 50
+```
+
+* Example usage:
+```
+    java -jar build/libs/bamscope.jar 18:53254446 ~/Downloads/x.bam -r ~/Downloads/x.fasta -o ~/Desktop/
+```
+
+## License
+
+Code and documentation released under the [MIT license](https://github.com/jslfree080/bamscope/blob/master/LICENSE).

.gradle/7.5.1/executionHistory/executionHistory.lock

@@ -73,6 +73,7 @@ tasks.withType<Jar> {
     // Otherwise you'll get a "No main manifest attribute" error
     manifest {
         attributes["Main-Class"] = "com.jslfree080.bamscope.RunBAMScopeKt"
+        archiveFileName.set("bamscope.jar")
     }
 
     // To avoid the duplicate handling strategy error
@@ -88,4 +89,4 @@ tasks.withType<Jar> {
 }
 
 // ./gradlew build |or| ./gradlew clean build (Delete all the previous version of the dependencies)
-// java -jar build/libs/bamscope*.jar 18:53253385 ~/Downloads/*.bam -r ~/Downloads/human_g1k_v37_decoy.fasta -o ~/Desktop/
+// java -jar build/libs/bamscope.jar 18:53253385 ~/Downloads/*.bam -r ~/Downloads/human_g1k_v37_decoy.fasta -o ~/Desktop/